OBJECTIVE: The objective was to determine if calcium intake was associated with resting energy expenditure (REE) and body fat in children after accounting for ancestral genetic background. STUDY DESIGN: Participants included 315 children. REE, body composition, and dietary calcium were assessed by indirect calorimetry, dual-energy x-ray absorptiometry, and 24-hour recalls, respectively. Structural equations modeling assessed the relationships among REE, calcium intake, and body fat. RESULTS: There were positive associations between calcium intake and REE (P<.01) and between REE and total body fat (P<.0001). There was indirect effect of calcium intake on total body fat (P<.01). There were positive associations between calcium intake and REE (P<.01), and a trend toward an association of calcium intake and total body fat (P=.065) among boys only, whereas the only significant relationship among girls was an association of REE on total body fat (P<.0001). CONCLUSIONS: REE was associated with calcium intake and mediated a relationship between calcium intake and total body fat. These findings suggest calcium intake may play a role in fat accumulation and energy balance through its effects on REE, especially in boys.